Software | Name | Version | Classification |
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HKL-2000 | | data collectionPHASER | | phasingPHENIX | (phenix.refine: 1.6_289)refinementHKL-2000 | | data reductionHKL-2000 | | data scaling | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→45.477 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0.08 / σ(I): 0 / Phase error: 19.14 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.1935 | 2864 | 5.07 % | random |
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Rwork | 0.1561 | - | - | - |
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obs | 0.158 | 56517 | 90.95 % | - |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.903 Å2 / ksol: 0.323 e/Å3 |
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Displacement parameters | | Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.8717 Å2 | -0 Å2 | 0 Å2 |
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2- | - | -0.8717 Å2 | 0 Å2 |
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3- | - | - | 1.7434 Å2 |
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Refinement step | Cycle: LAST / Resolution: 1.75→45.477 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 5024 | 0 | 26 | 755 | 5805 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.004 | 5233 | X-RAY DIFFRACTION | f_angle_d0.859 | 7110 | X-RAY DIFFRACTION | f_dihedral_angle_d13.385 | 1936 | X-RAY DIFFRACTION | f_chiral_restr0.061 | 812 | X-RAY DIFFRACTION | f_plane_restr0.004 | 929 | | | | | |
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LS refinement shell | Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Refine-ID | % reflection obs (%) |
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1.7501-1.8127 | 0.3044 | 156 | 0.2482 | 3317 | X-RAY DIFFRACTION | 56 | 1.8127-1.8853 | 0.2642 | 250 | 0.2086 | 4401 | X-RAY DIFFRACTION | 75 | 1.8853-1.9711 | 0.2365 | 263 | 0.1811 | 5272 | X-RAY DIFFRACTION | 90 | 1.9711-2.075 | 0.2096 | 309 | 0.1631 | 5597 | X-RAY DIFFRACTION | 95 | 2.075-2.205 | 0.1966 | 310 | 0.1551 | 5669 | X-RAY DIFFRACTION | 97 | 2.205-2.3752 | 0.1948 | 288 | 0.1499 | 5832 | X-RAY DIFFRACTION | 98 | 2.3752-2.6143 | 0.203 | 334 | 0.1543 | 5785 | X-RAY DIFFRACTION | 99 | 2.6143-2.9925 | 0.2024 | 324 | 0.1651 | 5856 | X-RAY DIFFRACTION | 100 | 2.9925-3.7699 | 0.1842 | 299 | 0.1458 | 5935 | X-RAY DIFFRACTION | 100 | 3.7699-45.492 | 0.1554 | 331 | 0.1331 | 5989 | X-RAY DIFFRACTION | 99 |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION ID | L11 (°2) | L12 (°2) | L13 (°2) | L22 (°2) | L23 (°2) | L33 (°2) | S11 (Å °) | S12 (Å °) | S13 (Å °) | S21 (Å °) | S22 (Å °) | S23 (Å °) | S31 (Å °) | S32 (Å °) | S33 (Å °) | T11 (Å2) | T12 (Å2) | T13 (Å2) | T22 (Å2) | T23 (Å2) | T33 (Å2) | Origin x (Å) | Origin y (Å) | Origin z (Å) |
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1 | 1.4328 | 0.3866 | -0.9229 | 1.4209 | -0.2775 | 1.0981 | 0.3114 | 0.5391 | -0.4264 | -0.3732 | 0.322 | 0.0249 | 0.2208 | 0.0313 | -0.4154 | 0.2117 | -0.0096 | -0.0307 | 0.178 | -0.0152 | 0.0841 | -69.5688 | 13.2411 | -17.8901 | 2 | 0.8866 | -0.0736 | 0.0389 | 0.1829 | -0.186 | 0.197 | 0.0028 | -0.0416 | -0.293 | 0.0533 | -0.0185 | -0.0816 | 0.1496 | 0.0818 | -0.03 | 0.1025 | 0.0091 | -0.0065 | 0.0289 | 0 | 0.0974 | -65.1883 | 8.2937 | -1.1737 | 3 | 0.9192 | 0.208 | 0.8395 | 1.2227 | -0.1701 | 3.0376 | 0.0048 | 0.2836 | -0.3115 | -0.2649 | 0.1454 | 0.4348 | 0.1254 | -0.4831 | -0.118 | 0.1637 | -0.0377 | -0.0424 | 0.1504 | -0.009 | 0.1785 | -75.009 | 9.1117 | -13.8393 | 4 | 1.19 | 0.466 | 0.1767 | 0.639 | 0.5097 | 1.644 | 0.1141 | 0.2375 | -0.2358 | -0.1072 | 0.1264 | -0.2963 | 0.0278 | 0.2803 | -0.2354 | 0.0816 | 0.007 | 0.0012 | 0.1156 | -0.0499 | 0.1428 | -55.7543 | 11.9303 | -9.7815 | 5 | 1.6098 | -0.3239 | 1.637 | 1.6653 | -1.6332 | 2.7339 | 0.0963 | 0.4172 | 0.0126 | -0.2479 | 0.1106 | 0.2237 | 0.3507 | 0.4479 | -0.1548 | 0.1469 | -0.0053 | -0.0216 | 0.1728 | -0.0045 | 0.0889 | -64.1237 | 16.8804 | -17.8333 | 6 | 1.0692 | 0.994 | -0.3136 | 1.4866 | 0.2212 | 1.0476 | 0.0113 | 0.1703 | 0.0481 | -0.1074 | 0.1818 | -0.0794 | -0.236 | 0.0808 | -0.1397 | 0.0885 | -0.013 | 0.0284 | 0.0741 | -0.0066 | 0.0726 | -57.7156 | 22.7763 | -11.1357 | 7 | 0.4541 | 0.0813 | 0.1153 | 0.6709 | -0.3695 | 0.7854 | 0.0577 | -0.0021 | 0.0358 | 0.1461 | 0.0305 | -0.0366 | -0.1801 | -0.0542 | -0.0695 | 0.1487 | 0.0103 | 0.0084 | 0.0462 | -0.0011 | 0.0676 | -67.5004 | 22.3086 | 7.1694 | 8 | 1.0295 | -0.1744 | 0.2154 | 0.5709 | -0.2838 | 0.1579 | -0.4002 | -0.1796 | 0.0481 | 0.2167 | -0.035 | 0.4499 | 0.0008 | -0.5759 | 0.4057 | 0.6275 | 0.074 | 0.0021 | 0.4273 | -0.1219 | 0.1684 | -72.6138 | 22.4407 | 34.7993 | 9 | 0.0299 | -0.1838 | -0.05 | 0.6129 | 0.0319 | 1.0177 | 0.0586 | -0.1006 | 0.0299 | 0.2851 | -0.0285 | -0.3202 | -0.2524 | 0.1607 | 0.0746 | 0.2446 | -0.032 | -0.0554 | 0.0917 | -0.0073 | 0.1113 | -61.391 | 22.3617 | 16.3812 | 10 | 0.8825 | 0.1704 | 0.0054 | 0.6584 | -1.1327 | 2.4579 | 0.0201 | 0.0666 | 0.2307 | 0.6448 | -0.0507 | -0.2489 | -0.7727 | -0.0406 | 0.1807 | 0.5955 | -0.0644 | -0.1589 | 0.1119 | -0.0232 | 0.1465 | -61.3111 | 25.916 | 29.2759 | 11 | 0.7807 | -0.2465 | 0.728 | 1.0769 | 0.1826 | 2.2203 | 0.0108 | 0.0122 | 0.0502 | 0.4047 | 0.0157 | -0.4903 | -0.1186 | 0.6357 | 0.0062 | 0.2324 | -0.0438 | -0.1377 | 0.1418 | -0.0099 | 0.2104 | -52.4601 | 15.1851 | 19.035 | 12 | 1.123 | -0.8906 | -0.1348 | 0.8098 | 0.0356 | 0.0679 | -0.0671 | -0.1365 | 0.0542 | 0.3639 | 0.1608 | -0.2444 | 0.038 | 0.2756 | -0.0374 | 0.2754 | -0.0168 | -0.0853 | 0.1098 | -0.0011 | 0.0964 | -59.8934 | 11.902 | 23.3639 | 13 | 0.9582 | 0.7706 | -0.2564 | 1.7952 | 0.4901 | 2.5858 | 0.0131 | -0.0474 | -0.274 | 0.5669 | 0.2289 | -0.5553 | 0.9879 | 0.1801 | -0.1486 | 0.5297 | -0.0023 | -0.193 | 0.0564 | 0.0252 | 0.1368 | -60.0153 | 4.0192 | 30.0244 | 14 | 0.4262 | -0.1889 | 0.2134 | 0.7038 | -0.7089 | 0.7322 | 0.0642 | -0.0401 | -0.1154 | 0.2059 | 0.009 | 0.0337 | 0.0632 | 0.0748 | -0.0711 | 0.153 | -0.0054 | -0.0094 | 0.0552 | 0.0173 | 0.0698 | -69.8026 | 7.8342 | 15.3209 | 15 | 0.0461 | -0.3173 | 0.3007 | 2.0418 | -2.0504 | 4.2764 | 0.0422 | 0.0794 | 0.0082 | -0.026 | 0.1167 | 0.4098 | -0.2856 | -0.3706 | -0.1106 | 0.0886 | 0.0176 | -0.0227 | 0.0947 | 0.0049 | 0.1167 | -76.0794 | 17.2636 | -6.6602 | 16 | 2.9445 | 0.0145 | -0.1365 | 4.1341 | 1.1971 | 3.8852 | 0.0126 | 0.629 | 0.0284 | -0.9124 | -0.1682 | 0.514 | -0.5183 | -0.5096 | 0.0655 | 0.2372 | 0.0481 | -0.0171 | 0.1685 | 0.0285 | 0.0941 | -76.538 | 25.915 | -10.4004 | 17 | 3.4009 | 1.9965 | -1.126 | 2.4327 | 0.0807 | 0.8084 | 0.4431 | 0.1216 | 0.7945 | 0.3178 | 0.0121 | 0.3318 | -0.2664 | -0.1253 | 0.2515 | 0.1682 | 0.0164 | 0.0891 | -0.0201 | 0.0074 | 0.1147 | -66.1899 | 32.1456 | 1.2891 | 18 | 1.2245 | 0.9823 | -0.6398 | 1.4019 | -0.8674 | 0.4935 | 0.1737 | -0.2999 | 0.3072 | 0.0094 | -0.138 | 0.2501 | -0.0815 | 0.0814 | -0.0599 | 0.1605 | 0.029 | 0.0453 | 0.0734 | 0.0122 | 0.1276 | -70.1736 | 27.5227 | -0.6621 | 19 | 0.4575 | -0.4422 | -0.2788 | 0.6194 | -0.1163 | 0.4439 | 0.0524 | -0.028 | -0.2137 | 0.1605 | -0.004 | 0.1399 | 0.0629 | -0.1216 | -0.0469 | 0.1439 | -0.0135 | 0.016 | 0.0738 | 0.0228 | 0.1238 | -78.4712 | 6.5411 | 13.4033 | 20 | 2.7732 | -0.8238 | -0.3145 | 0.3685 | 0.43 | 3.2856 | 0.2173 | -0.4938 | -0.1354 | 0.4509 | 0.3683 | 0.0015 | 0.4963 | 0.0844 | -0.4985 | 0.2149 | 0.0141 | -0.0388 | 0.0715 | 0.004 | 0.3224 | -75.9498 | -4.9205 | 10.7973 | 21 | 0.8687 | -0.4063 | 0.4254 | 1.8889 | 0.2259 | 0.4336 | 0.0599 | 0.2289 | -0.2568 | -0.4131 | 0.0231 | 0.1464 | 0.0273 | 0.0526 | -0.0276 | 0.1745 | 0.0312 | -0.0228 | 0.1281 | 0.0044 | 0.1431 | -89.7964 | 11.7066 | 5.9461 | 22 | 1.8042 | 0.5572 | -0.7211 | 1.629 | -2.8781 | 5.4884 | 0.0567 | -0.0746 | -0.9282 | -0.7428 | 0.0683 | -0.0565 | 1.4174 | 0.3047 | -0.0034 | 0.4521 | 0.098 | -0.0521 | 0.1229 | -0.0923 | 0.355 | -89.7506 | 1.6843 | 0.4664 | 23 | 1.1675 | -0.7076 | 0.6444 | 2.5511 | -0.5734 | 0.4238 | 0.0758 | 0.2595 | 0.0519 | -0.2295 | -0.072 | -0.2751 | 0.0907 | 0.1664 | 0.0056 | 0.203 | 0.0216 | -0.0035 | 0.1812 | 0.0213 | 0.1723 | -88.7476 | 19.2157 | 1.9031 | 24 | 2.5928 | -2.1864 | 1.0788 | 2.956 | -1.2295 | 0.569 | 0.3891 | 0.8703 | -0.0285 | -1.1266 | -0.6813 | -0.6434 | 0.2298 | 0.4202 | 0.2437 | 0.4248 | 0.0908 | 0.0324 | 0.3122 | 0.0084 | 0.1881 | -91.4887 | 19.4979 | -7.6949 | 25 | 0.7525 | 0.4934 | 0.8379 | 0.3765 | 0.5576 | 1.8432 | 0.1517 | 0.1023 | -0.0717 | 0.0522 | -0.0098 | 0.0531 | 0.2364 | -0.022 | -0.1459 | 0.1535 | 0.0307 | -0.0444 | 0.1573 | 0.0087 | 0.1825 | -97.0737 | 21.378 | 4.1975 | 26 | 2.8623 | -1.0909 | 0.4934 | 2.7377 | 0.0314 | 0.1581 | 0.1926 | 0.7869 | 0.1416 | -0.9645 | -0.0935 | 0.4481 | -0.5125 | -0.0415 | 0.0006 | 0.368 | 0.0942 | -0.1148 | 0.3113 | 0.0361 | 0.1827 | -100.5885 | 24.0552 | -6.1908 | 27 | 0.4622 | -0.1582 | 0.0222 | 1.3219 | -0.5578 | 0.3432 | 0.0792 | 0.1858 | -0.2952 | -0.1299 | 0.0274 | 0.6745 | 0.0019 | -0.163 | -0.1054 | 0.1826 | 0.0578 | -0.0625 | 0.1682 | -0.012 | 0.2873 | -103.0663 | 16.656 | 5.038 | 28 | 0.7015 | -0.6188 | 0.5471 | 1.489 | -1.3707 | 2.4807 | -0.1737 | -0.5497 | -0.6687 | 0.1986 | 0.6475 | 0.3745 | 0.2073 | -0.8124 | -0.4656 | 0.2687 | 0.1133 | 0.1066 | 0.3675 | 0.2275 | 0.3629 | -104.6874 | 11.3456 | 29.154 | 29 | 0.3298 | 0.2553 | 0.2014 | 0.6328 | 0.1795 | 0.1235 | 0.0531 | 0.1542 | 0.0339 | 0.1299 | 0.2526 | 0.1666 | -0.0258 | -0.1245 | -0.1718 | 0.6985 | 0.2841 | 0.4372 | 1.0864 | 0.4234 | 0.7264 | -108.99 | 10.9388 | 43.4012 | 30 | 2.6236 | 0.0697 | 0.5809 | 0.5056 | -0.423 | 0.7566 | -0.2137 | -0.7323 | -0.0388 | 0.3825 | 0.1909 | 0.3027 | -0.4485 | -0.4903 | -0.0592 | 0.3057 | 0.19 | 0.0909 | 0.368 | 0.0697 | 0.2349 | -105.4048 | 21.0383 | 28.4169 | 31 | 2.0415 | 0.8766 | -0.1501 | 2.3194 | -0.349 | 3.35 | -0.1439 | -0.6326 | 0.1844 | 0.4634 | -0.1276 | 0.6697 | -0.4656 | -0.7546 | 0.2365 | 0.414 | 0.2245 | 0.0998 | 0.462 | -0.0236 | 0.3247 | -104.399 | 27.0743 | 34.0736 | 32 | 0.5024 | 0.0748 | 0.3497 | 0.151 | 0.3631 | 0.7209 | -0.337 | -0.2279 | 0.3084 | 0.5038 | 0.0579 | -0.1244 | -0.3022 | 0.0572 | 0.2394 | 0.3732 | 0.0809 | -0.0685 | 0.1512 | 0.004 | 0.2178 | -92.7103 | 27.8808 | 28.1585 | 33 | 0.6721 | 0.177 | -0.7597 | 0.1947 | 0.6159 | 5.2654 | 0.2876 | -0.8899 | 0.4979 | -0.2839 | -1.8287 | 0.5161 | 1.3961 | 0.5326 | 1.2708 | 0.9454 | 0.1022 | -0.1529 | 0.6264 | -0.0866 | 0.1737 | -95.2423 | 26.3709 | 45.063 | 34 | 1.6733 | -1.0951 | 0.6004 | 1.8924 | -1.0374 | 0.7571 | -0.3875 | -0.4118 | -0.0382 | 0.5899 | 0.1634 | -0.0651 | -0.3238 | -0.2302 | 0.0625 | 0.3954 | 0.1283 | -0.0193 | 0.1778 | 0.0601 | 0.1406 | -90.399 | 15.2042 | 33.5346 | 35 | 1.0334 | -0.8474 | 0.3889 | 1.0918 | -0.7358 | 0.9522 | -0.0081 | -0.0799 | -0.3642 | 0.053 | 0.0994 | 0.3828 | 0.2174 | -0.1284 | -0.1844 | 0.181 | 0.0302 | -0.0154 | 0.0849 | 0.0519 | 0.2392 | -95.6273 | 6.0531 | 17.5234 | 36 | 1.9454 | 0.1361 | 0.531 | 0.4195 | 0.5342 | 2.5234 | 0.3584 | 0.8475 | -0.2243 | -0.4608 | 0.1535 | 0.6435 | 0.456 | -0.4435 | -0.3578 | 0.4522 | 0.0523 | -0.2587 | 0.3618 | -0.098 | 0.5057 | -104.8489 | 5.1676 | -3.0495 | 37 | 0.2639 | 0.5967 | 0.2234 | 2.3345 | -0.2409 | 1.4041 | 0.504 | 0.1172 | -0.479 | -0.2111 | -0.1554 | 0.3283 | 0.3255 | -0.2558 | -0.4239 | 0.1498 | 0.0468 | -0.0071 | 0.212 | 0.0942 | 0.5415 | -112.4439 | 14.8616 | 10.0859 | 38 | 1.0325 | 0.1329 | 0.6876 | 0.8133 | 0.449 | 1.1103 | 0.257 | 0.0009 | -0.5538 | -0.089 | 0.0823 | 0.8969 | 0.3682 | -0.0778 | -0.3715 | 0.1988 | 0.0264 | -0.0448 | 0.1608 | 0.0965 | 0.4759 | -105.0653 | 10.4443 | 14.0649 | 39 | 4.8972 | 0.7259 | -0.4579 | 0.3836 | -1.025 | 3.435 | 0.077 | -0.1189 | -1.0549 | 0.4609 | 0.2379 | 0.4443 | 0.5544 | -0.235 | -0.1215 | 0.2862 | 0.0085 | 0.025 | 0.0725 | 0.1643 | 0.4191 | -91.9299 | -2.2216 | 25.7027 | 40 | 3.5516 | -2.2964 | 0.8151 | 1.7006 | -0.4541 | 0.3264 | 0.3387 | -0.2274 | -0.9762 | -0.0952 | -0.1207 | 0.4971 | 0.142 | -0.1943 | -0.2611 | 0.2189 | 0.014 | -0.0111 | 0.1146 | 0.0602 | 0.2918 | -83.2816 | 0.7731 | 22.376 |
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Refinement TLS group | ID | Refine-ID | Refine TLS-ID | Selection details |
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1 | X-RAY DIFFRACTION | 1 | (chain A and resid 2:8)2 | X-RAY DIFFRACTION | 2 | (chain A and resid 9:26)3 | X-RAY DIFFRACTION | 3 | (chain A and resid 27:35)4 | X-RAY DIFFRACTION | 4 | (chain A and resid 36:57)5 | X-RAY DIFFRACTION | 5 | (chain A and resid 58:63)6 | X-RAY DIFFRACTION | 6 | (chain A and resid 64:86)7 | X-RAY DIFFRACTION | 7 | (chain A and resid 87:125)8 | X-RAY DIFFRACTION | 8 | (chain A and resid 126:131)9 | X-RAY DIFFRACTION | 9 | (chain A and resid 132:157)10 | X-RAY DIFFRACTION | 10 | (chain A and resid 158:172)11 | X-RAY DIFFRACTION | 11 | (chain A and resid 173:200)12 | X-RAY DIFFRACTION | 12 | (chain A and resid 201:219)13 | X-RAY DIFFRACTION | 13 | (chain A and resid 220:235)14 | X-RAY DIFFRACTION | 14 | (chain A and resid 236:265)15 | X-RAY DIFFRACTION | 15 | (chain A and resid 266:277)16 | X-RAY DIFFRACTION | 16 | (chain A and resid 278:288)17 | X-RAY DIFFRACTION | 17 | (chain A and resid 289:294)18 | X-RAY DIFFRACTION | 18 | (chain A and | | | | | | | | | | | | | | | | | |
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